The long-term objectives of this research are to understand the genetics of male infertility. The Collaborative Cross is a mammalian reference population that was designed to provide a cross-disciplinary platform for systems genetics in the most popular mammalian model organism, the mouse, and to overcome limitations of existing platforms. During the derivation of the Cross, approximately half of the lines are becoming extinct and male infertility is a major cause of lost lines. Characterization of males from the extinct lines provides a transient, but unique opportunity, for substantial genetic dissection of male infertility. We have assembled an expert group of scientists with complementary strengths in reproductive biology, genetics/genomics and computational biology and a strong record of productive collaborations to take full advantage of this window of opportunity. The surviving lines of the Collaborative Cross provide additional resources for validation and in-depth physiological and molecular analyses. Our specific aims are to: 1) complete the phenotypic characterization of males from extinct CC lines and genotype them with the high-density genotyping array; 2) identify loci associated with phenotypic variation for major male reproductive traits including abnormal testis histology, testis weight, sperm count, sperm motility and infertility; and 3) provide independent validation of the infertility loci mapped in the extinct funnels, conduct in-depth phenotypic analysis of males with genotypes associated with male infertility and identify the underlying molecular mechanisms leading to male infertility. )